Molecular Dynamics Study On Conformational Activation And Molecular Recognition Mechanism Of Proteins

Proteins are a part of material basis of life,performing a large variety of functions in life activities.Amino acids are the structural units that make up proteins with various structures and functions.Mutation on only one amino acid may completely change conformation and dynamics of a protein and further affect its recognition by other molecules.Besides,proteins can also be used as a drug or a carrier in drug delivery systems.Thus,proteins receive extensive research in chemistry,biology,pharmacy and medicine.Currently,understanding of proteins at molecular level is far from complete;mechanism of conformational change and activity caused by mutations or posttranslational modifications is not clear;processes of protein-protein interaction or molecular recognition of proteins need further study;applications of proteins as a target,a drug or even a carrier to deliver a drug attract a lot of research interest.Therefore,answers to these questions are meaningful to understand protein molecular machines and design new drug delivery systems in the futureIn this thesis,multiple-scale molecular simulations,including molecular dynamics simulations,free energy calculations,quantum chemical calculations as well as Poisson-Boltzmann continuum electrostatics,were employed to study conformations and dynamics of heat shock protein 90(Hsp90),ATP hydrolysis mechanism in Hsp90,activation mechanism and Hsp90-dependence of tyrosine kinase c-Src and its mutants c-Src3M?C and v-Src,delivery of interferon ?-1b(IFN)by bovine serum albumin(BSA)as carrier,and adsorption of BSA on different facets of SrTiO3 nanocrystals.1.Glu33 in Hsp90 is catalytically important for ATP hydrolysis and Arg380 could stablize the nagatively charged transition state of ATP.When Arg32 swings away from Glu33,protonation of Glu33 can be favored,leading to a lowered energy barrier.2.Phosphorylation on Ser379,Ser485,Ser602 and Ser604 could disturb dimerization of Hsp90,which might increase the interaction between ATP and the N-terminal domain.Mutation(Trp300Ala/Glu/Lys)on Trp300 makes the whole protein more compact and increases length of force propagation pathways in the three mutants.Mutation on Phe104 and Phe124 to Trp strengthens ?-? interaction between ATP and Phe or Trp,which further changes the conformation of the ATP binding site Mono-methylation on Lys594 at the constitutive dimerization interface results in a large conformational change at the C-terminal domain.3.Activation of the wild type tyrosine kinase c-Src is strictly controlled by ATP binding or phosphorylation on Tyr416.In the mutant c-Src3M?C,however,activating conformational transitions are spontaneously sampled without ATP binding or phosphorylation.Dynamic similarities between the mutant c-Src3M?C and the oncogenic v-Src indicate that the 3MAC mutations are the critical factor to turn c-Src to a mutant with much higher activity.4.Hsp90 recognizes unfolded structure in kinases,especially the ?1-?5 sheets and the P-loop.Hsp90 can stabilize an active protein in a metastable state,like c-Src3MAC as well as v-Src,while the stable c-Src is not Hsp90-dependent.5.A drug delivery system is designed in which IFN binds to BSA at the III domain.Hydrogen bonds and salt bridges play an important part in the interaction.Free energy calculations suggest that IFN shows higher affinity to BSA than small chemical drugs.6.The(100)and(110)facets of SrTiO3 show different protein adsorption behavior.The immobile surface hydration layer on the(110)facet might play a role as a barrier to prevent BSA adsorption,while protein can interact with SrTiO3 through the disordered hydration layer on the(100)facet.